The root and surrounding rhizosphere ecosystem is a dynamic and complex environment subject to the interaction of different microbial communities, which affect the outcome of the plant-phytobiome. In the root ecosystem, oomycetes are part of the microbial community and are some of the most aggressive and important plant pathogens. In the United States, soybeans are produced across 76 million acres of highly productive land, but can be severely impacted by diseases caused by oomycetes. We initially utilized a two-year culture based survey to study oomycetes associated with soybean seedlings from across 11 states in the Midwest, characterizing the communities and profiling phenotypic traits such as pathogenicity and aggressiveness. With this approach a total of 83 different oomycete species were identified and characterized. The survey served as a basis to develop markers and phenotypic data that could be used to further investigate and characterize oomycete communities associated with agricultural systems. We are currently utilizing this phenotype information and amplicon-based community analysis to evaluate the role of climatic, edaphic and biotic factors on the oomycete community structure. Improved understanding of the phytobiome, especially in the root system, and the factors that influence it will enable improved disease management and enhance plant health.